Depends on if you're talking about unlocking new ability's/perks. Or if you are talking about leveling up the perks themselves...
Getting your armor to a higher level will allow you to unlock to armor perks. Leveling the perks themselves will give you an added bonus when you have said perk selected.
For example. My Mobility perk at level 3 gives me the ability to climb up ledges faster and to fire faster when coming out of sprint on top of the base ability of using less energy.